| import/export {GSEABase} | R Documentation |
getBroadSets parses one or more XML files for gene sets. The
file can reside locally or at a URL. The format followed is that
defined by the Broad (below). toBroadXML creates Broad XML
from BroadCollection gene sets.
toGmt converts GeneSetColletion objects to a character
vector representing the gene set collection in GMT
format. fromGmt reads a file or other character vector into a
GeneSetColletion.
getBroadSets(uri, ...)
toBroadXML(geneSet, con, ...)
asBroadUri(name,
base="http://www.broad.mit.edu/gsea/msigdb/cards")
getGmt(con, geneIdType=NullIdentifier(),
collectionType=NullCollection(), sep="\t", ...)
toGmt(x, con, ...)
uri |
A file name or URL containing gene sets encoded following the Broad specification. For Broad sets, the uri can point to a MSIGDB. |
geneSet |
A GeneSet with
collectionType BroadCollection (to ensure that
required information is available). |
x |
A GeneSetCollection or other object for
which a toGmt method is defined. |
con |
A (optional, in the case of toXxx) file name or
connection to receive output. |
name |
A character vector of Broad gene set names, e.g.,
c('chr16q', 'GNF2_TNFSF10'). |
base |
Base uri for finding Broad gene sets. |
geneIdType |
A constructor for the type of identifier the members
of the gene sets represent. See GeneIdentifierType for
more information. |
collectionType |
A constructor for the type of collection for the
gene sets. See CollectionType for more information. |
sep |
The character string separating members of each gene set in the GMT file. |
... |
Further arguments passed to the underlying XML parser,
particularly file used to specify an output connection
for toBroadXML. |
getBroadSets returns a GeneSetCollection of gene sets.
toBroadXML returns a character vector of a single
GeneSet or, if con is provided, writes the XML to a
file.
asBroadUri can be used to create URI names (to be used by
getBroadSets of Broad files.
getGmt returns a GeneSetCollection of gene sets.
toGmt returns character vectors where each line represents a
gene set. If con is provided, the result is written to the
specified connection.
Actual Broad XML files differ from the DTD (e.g., an implied ',' separator between genes in a set); we parse to and from files as they exists the actual files.
Martin Morgan <mtmrogan@fhcrc.org>
http://www.broad.mit.edu/gsea/
## 'fl' could also be a URI
fl <- system.file("extdata", "Broad.xml", package="GSEABase")
gss <- getBroadSets(fl) # GeneSetCollection of 2 sets
names(gss)
gss[[1]]
## Not run:
## Download from the Broad
getBroadSets(asBroadUri(c('chr16q', 'GNF2_ZAP70')))
## End(Not run)
fl <- tempfile()
toBroadXML(gss[[1]], con=fl)
noquote(readLines(fl))
unlink(fl)
## Not run:
toBroadXML(gss[[1]]) # character vector
## End(Not run)
fl <- tempfile()
toGmt(gss, fl)
getGmt(fl)
unlink(fl)